itk-SNAP re-orient image

Chosing the correct image orientation is crucial for the registration to work. itk-SNAP let’s you change your image orientation manually using their Reorient Image tool. This tutorial will teach you how to use itk-SNAP to manually re-orient an image from LPI to ARI.

1. Load your image into itk-SNAP like you would normally do.

2. Under Tools select Reorient Image...

3. In the menu that will open, you will be presented with the current orientation of your image on the left, and the new orientation on the right.

4. To change the orientation either enter the RAI orientation code directly in the RAI Code: text field, or change the x, y and z axes of the image until the desired orientation is achieved. The preview window on the bottom right will give you an indication of where you are in 3D space.

5. Once the correct orientation has been confirmed and the changes are applied, the Reorient Image menu can be closed. Your image will now appear in the new orientation itk-SNAP’s main window.

6. Save the newly oriented image manually or click Save when exiting itk-SNAP. Click on Close without Saving if you don’t want to save the image in its new orientation.